Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CDX2

Cell type

Cell type Class
Digestive tract
Cell type
Caco-2
Primary Tissue
Colon
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Caco-2
cell type
Colorectal cancer cells
chip antibody
CDX2(Bethyl BL3194)
genotype
parental

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were cross-linked with 1% formaldehyde for 10 mins at 37°C, washed in cold PBS, resuspended in lysis buffer, and sonicated to obtain chromatin fragments between 200 bp and 1000 bp. Sonicated chromatin was resuspended in IP buffer, and incubated overnight at 4 °C with magnetic beads conjugated to CDX2 (Bethyl BL3194). The IP was washed 5 times with RIPA buffer and the DNA recovered by reversing the crosslink in 1% SDS, 0.1 M NaHCO3 for 8 h at 65°C. DNA was purified and quantified by Qubit. libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
75416889
Reads aligned (%)
92.5
Duplicates removed (%)
9.5
Number of peaks
5071 (qval < 1E-05)

hg19

Number of total reads
75416889
Reads aligned (%)
91.3
Duplicates removed (%)
9.7
Number of peaks
3400 (qval < 1E-05)

Base call quality data from DBCLS SRA